Honestly, if KH2 had been KH2FM instead, the game would have been much better for the fact that KH2FM at least had the complete vision Nomura said he wanted or whatever. However, even then we get a lot of faults in it that aren't exactly "best game eva" material.
-The prologue with Roxas was way too long in my opinion. I love Roxas, but God was it long. The only thing that saved it for me was Twilight Thorn and Axel. The prologue should have been shorter and had Roxas actually be the hero of the game instead/with Sora because I just felt that part went on longer than the opening credits for the Spider-Man movies.
-Kairi. Yeah, I don't like Kairi (at all), but I want Kairi to actually become a much better character than she was portrayed in KH2. From what we can infer, she never once mentions Riku until she reunites with him or the scene with Selphie, but she basically brushes him off even though he almost got eaten by a crazy pedo darkness Billy Zane. Then, she gets kidnapped three times: the first time with Axel, another Axel kidnapping when she escapes, and then Saix. Seriously?! Way to just shove her in the plot. Oh, and don't even get me started about her "fighting" scenes. Her character basically got downgraded (as did most of KH2's characters). BbS Kairi was better if for the fact she actually decided herself to sit this one out.
-Character development. Sora turns stupid, SDG feels peculiar whereas CoM SDG was probably my favorite representation ever of them, little of the Org. was shown even in FM so characters like Demyx, Luxord, and Xaldin felt ill-developed. Axel turns kind of... obsessive like Rachel in the middle of Season Two of Glee. The only characters I found that were solid and nice were Roxas (albeit crazy), Namine (thank god she got barely any screen time or else they may have ruined her), Rikunort/Riku and Mickey. Oh, and Auron.
-None of the worlds except original worlds connected. And even then, FF characters in said worlds have no place in the real plot. Basically, they took the things KH1 did (and CoM tried to emulate using memories) and tossed it out completely. The worlds felt more like side-quests rather than actually part of the game.
-Pixie YRP.
-Atlantica.
-The Keyblades were pretty iffy, even compared to BbS's which, while kind of nice, felt iffy due to repetition through characters.
-Barely any battles with the Org. until the end of the game.
-The world's stories should have been focused upon in one visit. Two visits made the game feel longer than it ever should have been.
-Platforming was gone completely, there was no strategy needed, magic system sucked, summons were pointless, and drives just made an already easy game easier. If anything Anti-Form saved that aspect since you could either a) revert, or b) play as Anti-Form but be careful not to get severely injured since you couldn't heal.
-Plot holes and unnecessary unanswered story details that could have gone in here.
The only redeeming factor was the (probably unintentional) SoRi scenes.
I can;t think of anymore right now but I'm sure I can later. And this is the fact that KH2 was the first KH I ever finished, and used to hate CoM which I had before it. But replaying CoM and then getting KH1, I realized just how bad KH2 is in the series. Even Re:coded which was entirely pointless had better writing and was an actually enjoyable game (Data Riku!) despite recycling worlds for the fortieth time. I love KH2, don't get me wrong. But it was bad. It's like the awkward pubescent age of the KH series. Though, I did like Sora and Riku's designs, which I wish we could see more often since, as much as I love the KH1 forms, I want to see something we haven't yet/as much.